mmg_233_2013_genetics_genomicswikiaorg-20200214-history
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
In this study, the scientists assembled and analyzed the genome of a female Tibetan wild boar. They also resequenced 30 Tibetan wild boards from six locations and 18 geographically related pigs in China. They characterized genetic diversity, population structure, and patterns of evolution. They compared the Tibetan wild boars to chinese domestic pigs and reported genetic adapatations in Tibetan wild boars associated with high altitudes and increased salivation in domestic pigs. Materials + Methods De novo sequencing methods were used and the genome was annotated. They also defined gene families and constructed a phyllogenetic tree to estimate divergence time between the Tibetan wild boar, Duroc pig, cattle, dog, mouse, and human. The expansion and contraction of the gene ortholog clusters were compared. The nonsynonymous to synonymous substitutions were estimated for each of the comparisons. The study exampled 188 pseudogenes in the Tibetan wild boar genome. They resequenced the population of pigs and performed SNP calling using a Bayesian approach. Phylogenetic and population genetics was analyzed and reconstructed the demographic history. They evaluated LD decay and quantified polymorphism levels. Results + Discussion The Tibetan wild boar has a higher proportion of lineage specific genes compared with the gene of the Duroc pig. Also, the Tibetan wild boar's genes has evidence of transcription which indicated new genes that have arisin since the two breeds diverged. The genes of the Tibetan wild boar were more adapted to natural selective pressure to adapt to harsh environments while the Duroc genes were better suited for innate immunity and probably better response to a large array of food types. It is believed that the Tibetan wild boar and Durac pig divered about 6.9 million years ago which was earlier than when the yak and cattle diverged and around the time humans and chimpanzees diverged. The Tibetan wild boar shows more gene expansion of the ferritin gene family while the Duroc pig has more olfactory related genes. This corresponds with the habitat that Tibetan wild boars live in which are at high altitudes. The higher altitudes yield less diversity of food and thus less chemical signals in the air. The interactions of odourants and receptors are weaked in high altitude environments. For the Duroc pig, the high number of olfactory genes signifies that it relies on the sense of smell heavily. This high number of genes allows the Duroc pig to recognize a large variety of odors. Living at high altitudes, it was found that the Tibetan wild boar had stronger adaptation to hypoxic environments compared to the Duroc pig. Genes found were involved in morphogenesis of blood vessels, development of blood vessels, hypertrophic cardiomyophathy, and heart development. With regard to DNA damage, The Tibetan wild boar is more adapted to coping with intensive solar ultraviolet radiation induced DNA damage. They had more genes in the response to DNA damage stimulus category, damaged DNA binding, DNA repair protein, and positive regulation of DNA replication. This is compared to none in the Duroc pig. The Tibetan wild boar and the Chinese domestic pig were also compared and found that the regions that are affected by natural selection in Tibetan wild boars are smaller than those affected by artificial selection in domestic pigs.The Chinese domestic pig had lower levels of polyomrphism. Portions of the pig's genomes have remained distinctly adapted to natural or artificial selection. The study of the the Tibetan wild boar, Duroc pig, and Chinese domestic pig provides insight into the evolutionary scenarios occuring under natural and aritificial selection. Reference 1. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars